Functional annotation of the Arabidopsis genome using controlled vocabularies

Plant Physiology

Volumn 135, Issue 2, 2004, Pages 745-755

  Berardini, Tanya Z ^a   Mundodi, Suparna ^a   Reiser, Leonore ^a   Huala, Eva ^a   Garcia Hernandez, Margarita ^a   Zhang, Peifen ^a   Mueller, Lukas A ^a,c   Yoon, Jungwoon ^a   Doyle, Aisling ^a   Lander, Gabriel ^a   Moseyko, Nick ^a,b   Yoo, Danny ^a   Xu, Iris ^a   Zoeckler, Brandon ^a   Montoya, Mary ^b   Miller, Neil ^a,b   Weems, Dan ^b   Rhee, Seung Y ^a  

^a GEOPHYSICAL LABORATORY   (United States)

^b NATIONAL CENTER FOR GENOME RESOURCES   (United States)

^c Cornell University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE; DATA REDUCTION; GENES; PHYSIOLOGY; PLANTS (BOTANY);

DATA QUALITY; FUNCTIONAL ANNOTATIONS;

GENETIC ENGINEERING;

ARABIDOPSIS; EMBRYOPHYTA;

EID: 3042672020     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.104.040071     Document Type: Article

References (15)

1. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
2. Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R (2003) The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res 13: 662-672
3. Consortium GO (2001) Creating the gene ontology resource: design and implementation. Genome Res 11: 1425-1433
4. Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, et al (2002) Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res 30: 69-72
5. Emanuelsson O, Nielsen H, Brunak S, Svon Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016
6. Frishman D, Albermann K, Hani J, Heumann K, Metanomski A, Zollner A, Mewes HW (2001) Functional and structural genomics using PEDANT. Bioinformatics 17: 44-57
7. Hazbun TR, Malmstrom L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, et al (2003) Assigning function to yeast proteins by integration of technologies. Mol Cell 12: 1353-1365
8. Hennig S, Groth D, Lehrach H (2003) Automated Gene Ontology annotation for anonymous sequence data. Nucleic Acids Res 31: 3712-3715
9. Kanapin A, Batalov S, Davis MJ, Gough J, Grimmond S, Kawaji H, Magrane M, Matsuda H, Schonbach C, Teasdale RD, Yuan Z (2003) Mouse proteome analysis. Genome Res 13: 1335-1344
10. King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP (2003) Predicting phenotype from patterns of annotation. Bioinformatics 19 (suppl. 1): 1183-1189
11. Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD (2004) MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 32: D438-D442
12. MASC Committee (2003) The Multinational Coordinated Arabidopsis thaliana Functional Genomics Project: Annual Report 2003. MASC Committee, Madison, WI
13. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, et al (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 31: 315-318
14. Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M (2003) The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res 31: 241-243
15. Wortman JR, Haas BJ, Hannick LI, Smith RK Jr, Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, et al (2003) Annotation of the Arabidopsis genome. Plant Physiol 132: 461-468